Solving protein folding in your lunch break

While you take time out to eat your lunch, your computer could be busy helping crack one of the biggest challenges of modern biology.

By Andrew McLaughlin | October 25, 2000

LONDON. Understanding how proteins fold themselves into complex shapes is vitally important in comprehending how they work. But generating enough computer power to model folding in larger proteins is a feat beyond even the fastest of today's computers.

To help solve the problem, a team of researchers from Stanford University has set up folding@home, a computer network that enlists the help of idle computers around the world to simulate the folding process and distribute the results free of charge. By downloading a simple screen saver from the folding@home website, volunteers can contribute their computers' spare time to the project and help build an international super-computer capable of modeling these complex molecules as they self-assemble.

The idea of enlisting idle computers through the internet has been borrowed from another processing-heavy project — one that is searching for extraterrestrial intelligence. The SETI@home project uses the volunteer concept to analyze radio wave signals detected by a central receiver at Arecibo. Since its launch three years ago, the SETI computer has grown to become the largest in the world because it has successfully enlisted thousands of volunteers keen to take part in the search for extraterrestrial life.

Biology's equivalent of the SETI project will need to involve up to 100,000 volunteers in order to carry out the complex task of processing all of the available protein data. "Folding@home is considerably more complex than SETI@home," says Vijay S. Pande, head of the team at Stanford. "SETI just gives out work from a stack, we're doing dynamics which means that current work affects future work units." The project has already signed up more than 5,000 volunteers including members of the general public, "The public is excited about genomics and proteomics and people seem to be interested in taking part," says Pande.

One commercial organisation putting considerable resources into modelling protein folding is IBM, which is in the process of building a single computer capable of modelling protein folding on its own. Initial calculations suggest that the processing speed required for the computer, named Blue Gene by developers, is up to one quadrillion operations per second — 500 times the processing power of today's fastest machines. "If this machine unlocks the mystery of how proteins fold, it will be an important milestone in the future of medicine and healthcare," says Dr Paul M. Horn, senior vice president of research at IBM.

By comparison, even with 100,000 volunteers, the processing power of the folding@home project will still be smaller than Blue Gene, says Pande. "Even if we had a million volunteers, we'd only just be comparable."

Key goals for the folding@home project include demonstrating how proteins fold and gaining an understanding of the physical and chemical mechanisms involved. This, it is hoped, will give an insight into the events that can cause a protein to misfold and clump together — a phenomenon believed to cause the symptoms of both Alzheimer's disease and Bovine Spongiform Encephalopathy. The Stanford team also hopesto understand how proteins fold so quickly and reliably, in order to learn how to make synthetic polymers that could be used in nanomachines and other protein-scale devices. The folding@home project team is already looking to publish some initial results, even though the first of the proteins has not yet been completely folded. After this initial phase, the team will begin working on larger proteins and developing drug design projects.

Volunteers for the project can register their interest at the folding@home website and, by setting the screensaver to come on when they are not at the desk or in their laboratory, can contribute vital data to the research project — even if it is only during a short coffee break. "The program allows you to run for as little or as long as you like," says Pande. "Even a single day's worth of running is helpful to us." Once the findings of the research are published, the Stanford team promises to make the raw data of the project available free of charge on the folding@home website.

It is also possible to register your assistance to the project as part of a team, so that your collective input to the project can be recorded. If you'd like to join the BioMedcentral folding@home team, download the folding@home screensaver software from the site below, and when you install it, put (BMC) at the end of your username (for example, Joe Bloggs (BMC)). Your efforts will then automatically count towards BioMedcentral's team total — and will show your support for BioMedcentral and freedom of information in publishing.